tbuckley/cabot-search huggingface dataset:
Abstract 5079: Comparative proteome analysis for predicting the prognosis of trastuzumab-based therapy
Authors: Juin Park, Woo Sun Kwon, Sun Kyoung Kang, Tae Soo Kim, Jihyun Hwang, Sang Woo Cho, Kyunggon Kim, Hyun Cheol Chung, Sun Young Rha
Journal: Cancer Research (2022)

Abstract Trastuzumab, a HER2-targeting antibody, has markedly altered the clinical course of the disease in HER2 + gastric cancer, which is 10-15% of metastatic GC. However, the majority of patients develop resistance within one year of treatment. Therefore, understanding the mechanisms of trastuzumab resistance is urgently needed to overcome trastuzumab resistance. This study explored the characteristics of trastuzumab resistant cell lines through comparative proteome analysis. We previously reported establishment of four trastuzumab resistant cell lines from HER2 amplified GC cell lines by trastuzumab dose-escalation treatment; YCC-33TR, YCC-38TR, NCI-N87TR, and SNU-216TR. Formalin-fixed paraffin-embedded tissue samples were obtained 10 GC patients prior to trastuzumab therapy. The patients were first stratified into poor and good responders based on whether their tumors had or had not progressed. For analysis of differentially expressed proteins (DEPs), label-free quantitative proteomic profiling was performed using high-resolution LC-MS system. Gene ontology (GO) and KEGG pathway enrichment analyses were conducted using DAVID database. Consistent with the previous results, we found that HER2 expression in TR cell lines remained as high as parental cell lines, also in proteomic profiling. As a result of proteomic analysis, total 5285 proteins were identified in 4 parental and 4 TR cell lines; 4854 common proteins, while 55 proteins unique to parental cell lines and 58 proteins unique to TR cell lines. Then, we did the hierarchical clustering with these DEPs to identify protein expression patterns. We observed that 129 and 62 proteins were upregulated in parental and TR cell lines, respectively (p&amp;lt;0.05). We identified C5orf51 and CENP-E, poor prognostic factors, were upregulated 200-fold in TR cell lines. Interestingly, we found that HLA-B, ITM2C, and PPP1R3D were highly expressed in TR cell lines and trastuzumab poor responders. In conclusion, we performed comparative proteome analysis in parental and TR cell lines and investigated the corresponding expression change. It may gain further novel insights into the mechanisms of trastuzuamb resistance. Citation Format: Juin Park, Woo Sun Kwon, Sun Kyoung Kang, Tae Soo Kim, Jihyun Hwang, Sang Woo Cho, Kyunggon Kim, Hyun Cheol Chung, Sun Young Rha. Comparative proteome analysis for predicting the prognosis of trastuzumab-based therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5079.
Abstract 3265: Discovery of a first-in-class reversible DNMT1-selective inhibitor
Authors: Melissa B. Pappalardi
Journal: Cancer Research (2022)

Abstract DNA methylation, a key epigenetic driver of transcriptional silencing, is universally dysregulated in cancer. Reversal of DNA methylation by hypomethylating agents, such as the cytidine analogs decitabine or azacytidine, has demonstrated clinical benefit in hematologic malignancies. These nucleoside analogs are incorporated into replicating DNA where they inhibit DNA cytosine methyltransferases DNMT1, DNMT3A, and DNMT3B through irreversible covalent interactions. These agents induce significant toxicity to normal blood cells thus limiting their clinical doses. We report the discovery of a series of potent first-in-class DNMT1-selective inhibitors that compete with the active-site loop of DNMT1 for penetration into hemi-methylated DNA. These compounds induce robust loss of DNA methylation, transcriptional activation, and cancer cell growth inhibition in vitro leading to superior tumor regression and survival in mouse models of acute myeloid leukemia due to improved in vivo tolerability compared with decitabine. Citation Format: Melissa B. Pappalardi. Discovery of a first-in-class reversible DNMT1-selective inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3265.
Abstract 187: High-throughput screening of cancer spheroids demonstrates sensitivity to combination chemotherapy
Authors: Elad Katz, Maureen R. Deehan, Russell D. Petty, Paul Davies
Journal: Cancer Research (2022)

Abstract We have designed and manufactured a miniaturized 3D cell culture format called NaviPlate. The NaviPlate contains a novel geometry to support the generation of cancer spheroids for robust and sensitive complex biological assays. Cells added to the NaviPlate spontaneously form spheroids, consistent with the cell line phenotype reported in the literature when using U-bottom multi-well formats. In addition, we have been able to perform assays such as cytotoxicity with a minimum number of 200 cells/well, representing a 5-50-fold improvement on existing 3D cell culture assays.Using the NaviPlate, we examined the response to chemotherapy of four commonly used cancer cell lines: LNCaP, AR mutant lymph-node derived prostate cancer; A549, KRAS mutant/EGFR wt NSCLC; HCT116, KRAS mutant/p53 wt colon cancer; and MDA-MB-231 triple negative breast cancer. First, the lines were exposed to three types of chemotherapy with distinct modes of action: 5-FU (DNA damage), Docetaxel (inhibition of microtubular polymerization) and Flavopiridiol (pan-CDK inhibition). Except for Flavopiridiol in A549 cells, all cell lines were resistant to chemotherapy, when grown in 3D, inside the NaviPlate. Furthermore, we were able to show that this resistance was dependent on the 3D formation of spheroids, as HCT116 cells exposed to chemotherapy before forming spheroids were still sensitive to treatment. Interestingly, in A549 cells, which form less tight spheroids, the effect of 3D clustering was less profound on the response to monotherapy. Lastly, we explored NaviPlate as a platform to identify best chemotherapy combination partners. We combined the three chemotherapies in all cell lines, with most combinations efficiently killing the spheroids. On note, the commonly used combination of 5-FU and Docetaxel had no statistically significant effect on the viability of either A549 or MDA-MB-231 cells.In conclusion, NaviPlate is an easy to use, cancer spheroid platform for the identification of chemotherapy combination partners and thus a useful tool for exploring personalized oncology approaches in the clinic. Citation Format: Elad Katz, Maureen R. Deehan, Russell D. Petty, Paul Davies. High-throughput screening of cancer spheroids demonstrates sensitivity to combination chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 187.
Abstract 808: <i>In vivo</i> targeting of replication protein A for cancer therapy
Authors: Pamela VanderVere-Carozza, Navnath Gavande, Shadia Jalal, Karen Pollok, Elmira Ekinci, Joshua Heyza, Steve Patrick, Andi Masters, John Turchi, Katherine Pawelczak
Journal: Cancer Research (2022)

Abstract Replication protein A (RPA) plays essential roles in DNA replication, repair, recombination and the DNA-damage response (DDR). Retrospective analysis of lung cancer patient data demonstrates high RPA expression as a negative prognostic biomarker for overall survival in smoking-related lung cancers. Similarly, relative expression of RPA is a predictive marker for response to chemotherapy. These observations are consistent with the increase in RPA expression serving as an adaptive mechanism that allows tolerance of the genotoxic stress resulting from carcinogen exposure. We have developed second generation RPA inhibitors (RPAi’s) that block the RPA-DNA interaction and optimized formulation for in vivo analyses. Data demonstrate that unlike first generation RPAi’s, second generation molecules with increased cellular permeability, induce cell death via apoptosis. Second gen RPAi’s elicit single agent in vitro anticancer activity across a broad spectrum of cancers and the cellular response supports a threshold exists before chemical RPA exhaustion induces cell death. Chemical RPA inhibition potentiates the anticancer activity of a series of DDR inhibitors as well as traditional DNA damaging cancer therapeutics. Consistent with the chemical RPA exhaustion model, we demonstrate that the effects of RPAi on replication fork dynamics. An optimized formulation was developed that resulted in single agent anticancer activity in two non-small cell lung cancer models. These data demonstrate a unique mechanism of action of RPAi’s eliciting a state of chemical RPA exhaustion can provide an effective therapeutic option for difficult to treat lung cancers. Citation Format: Pamela VanderVere-Carozza, Navnath Gavande, Shadia Jalal, Karen Pollok, Elmira Ekinci, Joshua Heyza, Steve Patrick, Andi Masters, John Turchi, Katherine Pawelczak. In vivo targeting of replication protein A for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 808.
Abstract 1097: First-line therapy based on kinase inhibitors and antibodies prevents resistance in EGFR-mutated lung cancer
Authors: Ilaria Marrocco, Yuya Haga, Yosef Yarden
Journal: Cancer Research (2022)

Abstract Introduction: Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are commonly used to treat patients with EGFR+ non-small cell lung cancer (NSCLC). Unfortunately, despite the initial response, the long-term efficacy of the five clinically approved TKIs (i.e., gefitinib, erlotinib, afatinib, dacomitinib, osimertinib) is limited by the onset of resistance. Several mechanisms of resistance have been described, including the appearance of new EGFR mutations (e.g., T790M, C797S), activation of bypass pathways (e.g., AXL, HER2, MET and IGF1R) and phenotypic alterations (e.g., epithelial to mesenchymal transition, EMT). Additionally, in vitro treatment using EGFR TKIs leads to the establishment of drug tolerant persisters (DTPs), a cell population that might be responsible for the onset of resistance. In order to prevent resistance, the data we present herein propose to simultaneously target EGFR and other survival receptors (e.g., HER2 or HER3) by combining TKIs and specific monoclonal antibodies. Materials and methods: Cultures of NSCLC cell lines, patient-derived and cell line xenografts were employed to test the efficacy of the drug combinations. In parallel, to better understand resistance to EGFR-TKIs we established NSCLC dacomitinib resistant (DR) cell lines that were used in vivo and in vitro. Results: DR cells showed upregulation of AXL and IGF1R, features shared with the persister cells. We also demonstrate that combining TKIs and monoclonal antibodies successfully prevented TKI acquired resistance, by downregulating receptor kinases previously implicated in resistance to TKIs (e.g., MET and AXL), as well as by blocking pathways essential for mitosis (e.g., FOXM1). Conclusions: Combining kinase inhibitors and antibodies in first line settings effectively avoids TKI resistance in animal models of lung cancer and might represent a long-term solution for EGFR positive NSCLC patients. Citation Format: Ilaria Marrocco, Yuya Haga, Yosef Yarden. First-line therapy based on kinase inhibitors and antibodies prevents resistance in EGFR-mutated lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1097.
Abstract 922: Knockout of <i>Sod2</i> accelerates formation of pancreatic atypical flat lesions which are a direct precursor to pancreatic ductal adenocarcinoma (PDA)
Authors: Alicia K. Fleming Martinez, Brandy H. Edenfield, Irene Esposito, Peter Storz
Journal: Cancer Research (2022)

Abstract Manganese superoxide dismutase (MnSOD) is an important reactive oxygen species (ROS) scavenger which has largely been studied in pancreatic cancer cell lines, where it contributes to invasion but also decreases proliferation. In pancreatic cancer, it is unknown whether MnSOD contributes to or prevents lesion development. Therefore, we utilize a transgenic mouse model to study precancerous lesion development and progression. We here show that knockout of Sod2 in a p48Cre;LSL-KrasG12D (KC) mouse model accelerates formation of abnormal tissue area, increases abundance of DCLK1+ cancer stem cells (CSCs) and oxidative damage, and promotes formation of atypical flat lesions (AFLs) which are a direct precursor to pancreatic ductal adenocarcinoma (PDA). We further characterize AFLs as having fewer senescent cells and less oxidative damage than low grade PanIN lesions. Thus, MnSOD has a protective effect in early pancreatic lesion development and its deletion drives tumor development. Citation Format: Alicia K. Fleming Martinez, Brandy H. Edenfield, Irene Esposito, Peter Storz. Knockout of Sod2 accelerates formation of pancreatic atypical flat lesions which are a direct precursor to pancreatic ductal adenocarcinoma (PDA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 922.
Abstract 1520: Replication stress and the inability to repair damaged DNA, the potential “Achilles' heel” of ecDNA+ tumor cells
Authors: Sudhir Chowdhry, Salvador Garcia, Nam-Phuong Nguyen, Anthony Celeste, Edison Tse, Snezana Milutinovic, Deepti Wilkinson, Christian Hassig, Shailaja Kasibhatla
Journal: Cancer Research (2022)

Abstract Replication stress (RS) is a primary source of genomic instability, tumorigenesis, and cancer progression. RS is defined as an uncoupling of the replicative helicase and DNA polymerase, resulting in long stretches of fragile single stranded DNA (ssDNA) that is prone to damage. Excessive RS can result in replication catastrophe and cell death, which could be leveraged as a therapeutic strategy to treat high-RS cancers. While overexpression of certain oncogenes has been implicated as a driver of RS in cancer, the precise cellular conditions that result in RS have been difficult to predict. Here we demonstrate that high copy number amplification of genes on non-native extrachromosomal DNA (ecDNA) is associated with elevated RS in comparison to the same amplification on linear chromosomes. The ecDNA bearing cells display heightened basal levels of phosphorylated RPA, a hallmark of ssDNA, and decreased replication fork velocities. Consistent with this finding, the ecDNA amplified cells display greater sensitivity to inhibitors of deoxyribonucleotide production relative to cells harboring chromosomal gene amplification and to normal cells. Moreover, ecDNA bearing cells demonstrate a dramatic vulnerability to reduction in the conditionally essential amino acid glutamine, the primary nitrogen source for de novo nucleotide biosynthesis. The enhanced sensitivity to glutamine starvation is directly correlated with a reduction in ecDNA in tumor cells, and a corresponding selection for chromosomally integrated gene amplification in the surviving population. These phenotypes are rescued with nucleoside supplementation but not anaplerotic TCA cycle intermediates, further reinforcing a link between ecDNA and RS biology. Collectively, observations made here support a novel mechanism for oncogene-induced RS shaped by ecDNA driven oncogene amplification, revealing a novel molecular strategy to identify high-RS tumors and a therapeutic approach to target this “Achilles heel” of tumor biology. Citation Format: Sudhir Chowdhry, Salvador Garcia, Nam-Phuong Nguyen, Anthony Celeste, Edison Tse, Snezana Milutinovic, Deepti Wilkinson, Christian Hassig, Shailaja Kasibhatla. Replication stress and the inability to repair damaged DNA, the potential “Achilles' heel” of ecDNA+ tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1520.
Abstract 2415: Loss of Krüppel-like factor 4 facilitates disruption of epithelial barrier function in gastric cancer and promotes metastasis
Authors: Sandeep Goswami, Chandrani Sarkar, Wendy L. Frankel, Sujit Basu, Debanjan Chakroborty
Journal: Cancer Research (2022)

Abstract Stomach or gastric cancer (GC) is one of the most common malignancies observed in men and women worldwide. It is also a leading cause of cancer-related deaths. The disease is potentially curable when diagnosed early with survival records of more than 90%. This number, however, sharply declines to less than 20% when diagnosed at advanced stages. Therefore identification of functional molecular markers that can predict the progression of the disease is of utmost importance as early diagnosis enhances the chances of successful therapeutic intervention. Krüppel-like Factors (KLFs) are a family of evolutionarily conserved transcriptional regulators with zinc finger DNA binding domains. KLFs have been shown to play important roles both in normal development as well as in disease progression. In cancers, KLFs have been reported to regulate diverse cellular processes like cell growth, proliferation and differentiation. Of the 17 KLFs identified to date, KLF4 and KLF 5 show significantly altered expression in GC tissues compared to normal gastric tissues (TCGA sample analysis of gene expression pattern for KLFs). WhileKLF5 typically pro-proliferative and acts as a tumor promoter, KLF4 has been both oncogenic and tumor-suppressive. KLF4 downregulation is associated with a poor prognosis in GC. However, the specific role of KLF4 in GC progression has not been fully elucidated. Using human GC tissues, orthotropic gastric tumors developed in athymic nude mice, and in vitro functional assays, we hereby report that loss of KLF4 in GC disrupts tight junction stability of epithelial cells. Loss of KLF4 expression correlates with altered expression of tight junction proteins such as claudins and ZO1 in GC. Altered expression of these proteins results in disruption of epithelial barrier integrity leading to cell detachment and metastasis. Therefore, our work indicates that loss of KLF4 observed in GC may promote cell metastasis and can serve as a prognostic marker for GC metastasis. The knowledge generated from this study not only imparts insight into the pathogenesis of GC metastasis but also will be helpful in the development of newer treatment strategies in the future. Citation Format: Sandeep Goswami, Chandrani Sarkar, Wendy L. Frankel, Sujit Basu, Debanjan Chakroborty. Loss of Krüppel-like factor 4 facilitates disruption of epithelial barrier function in gastric cancer and promotes metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2415.
Abstract 5681: Metabolic targeting of NRF2 potentiates the efficacy of TRAP1 inhibitor GTPP in colorectal cancer
Authors: Hong-Yuan Tsai, Ru Chen, Noah Shroyer, Sheng Pan
Journal: Cancer Research (2022)

Abstract Tumor necrosis factor receptor-associated protein 1 (TRAP1) is a mitochondrial homolog of HSP90 chaperones. It plays an important role in protection against oxidative stress and apoptosis by regulating reactive oxidative species (ROS) and may also exert the cytoprotective activities by regulating mitochondrial permeability transition pore opening. Recent studies have suggested that TRAP1 may regulate metabolism and mitochondrial homeostasis in cancer. To further elucidate the mechanistic role of TRAP1 in regulating tumor cell survival, we used cellular models to investigate cellular effects and signaling pathways regulated by TRAP1 in several colon cancer cell lines. Inhibition of TRAP1 by a small molecule inhibitor, Gamitrinib-triphenylphosphonium (GTPP), in colon cancer cells led to ROS production, ER stress, reduction of cell viability and induction of cell death. Interestingly, we observed wide-range of responses to TRAP1 inhibition among these colon cancer cell lines. In GTPP sensitive cell lines (SW48), GTPP induced upregulation of GRP78, CHOP and cleavage form PARP proteins. In contract, in GTPP resistant cells (DLD1 and RKO), GTPP treatment highly induced activation of antioxidant gene NRF2, leading to better cell survival under oxidative environment. NRF2 target genes HO1 and NQO1 were upregulated in GTPP-treated DLD1 cells, making these cells more resistant to GTPP treatment. Using reporter assay, we further found that transcriptional activation of antioxidative responds element (ARE) was increased in GTPP-treated DLD1 and RKO cells (GTPP resistant), but not in SW48 cells (GTPP sensitive). Combination of NRF2 inhibitor ML385 and GTPP led to excessive ROS production and exacerbated GTPP-induced cell death in GTPP resistant cells. These new findings for the first-time link TRAP1 and NRF2 in a common pathway regulating ROS production in colon cancer. Taken together, dual targeting of TRAP1 and NRF2 may potentially overcome the tumor cell resistance through disruption of mitochondrial redox homeostasis. Citation Format: Hong-Yuan Tsai, Ru Chen, Noah Shroyer, Sheng Pan. Metabolic targeting of NRF2 potentiates the efficacy of TRAP1 inhibitor GTPP in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5681.
A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication
Authors: Parul Johri, Jean-Francois Gout, Thomas G Doak, Michael Lynch
Journal: Molecular Biology and Evolution (2022)

Abstract Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for the long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand the selective forces acting on paralogs and investigate ongoing duplicate-gene loss in multiple species of Paramecium that share an ancient WGD. We show that mutations that abolish protein function are more likely to be segregating in retained WGD paralogs than in single-copy genes, most likely because of ongoing nonfunctionalization post-WGD. This relaxation of purifying selection occurs in only one WGD paralog, accompanied by the gradual fixation of nonsynonymous mutations and reduction in levels of expression, and occurs over a long period of evolutionary time, “marking” one locus for future loss. Concordantly, the fitness effects of new nonsynonymous mutations and frameshift-causing indels are significantly more deleterious in the highly expressed copy compared with their paralogs with lower expression. Our results provide a novel mechanistic model of gene duplicate loss following WGDs, wherein selection acts on the sum of functional activity of both duplicate genes, allowing the two to wander in expression and functional space, until one duplicate locus eventually degenerates enough in functional efficiency or expression that its contribution to total activity is too insignificant to be retained by purifying selection. Retention of duplicates by such mechanisms predicts long times to duplicate-gene loss, which should not be falsely attributed to retention due to gain/change in function.